FOXA2 rewires AP-1 for transcriptional reprogramming and lineage plasticity in prostate cancer

FOXA family proteins act as pioneer factors by remodeling compact chromatin structures. FOXA1 is crucial for the chromatin binding of the androgen receptor (AR) in both normal prostate epithelial cells and the luminal subtype of prostate cancer (PCa). Recent studies have highlighted the emergence of FOXA2 as an adaptive response to AR signaling inhibition treatments. However, the role of the FOXA1 to FOXA2 transition in regulating cancer lineage plasticity remains unclear. Our study demonstrates that FOXA2 binds to distinct classes of developmental enhancers in multiple AR-independent PCa subtypes, with its binding depending on LSD1. Moreover, we reveal that FOXA2 collaborates with JUN at chromatin and promotes transcriptional reprogramming of AP-1 in lineage-plastic cancer cells, thereby facilitating cell state transitions to multiple lineages. Overall, our findings underscore the pivotal role of FOXA2 as a pan-plasticity driver that rewires AP-1 to induce the differential transcriptional reprogramming necessary for cancer cell lineage plasticity.


May 20, 2024
Raw Illumina output was converted to to fastq format using Illumina Bcl2fastq The ChIP-seq (and ATAC-seq) reads were mapped to to the hg19 human genome using bwa (version 0.7.17-r1188) with the aln and sampe subcommands.Samtools (version 1.9) was used to to convert sam files to to bam format.Enriched ChIP regions were evaluated using MACS2 (version 2.1.4)(49).The Intervene (version 0.6.5) was used to to analyze peak intervals, determine overlapped regions, and generate Venn diagrams.The signals associated with genomic regions were visualized using compueMatrix and plotHeatmap tools from deepTools (version 3.3.0).computeMatrix was used to to calculate scores for each genomic region and plotHeatmap was used to to create a heatmap for scores associated with genomic regions.Motif enrichment analysis was performed using SeqPos with default settings.Binding and Expression Target Analysis (BETA) was performed using the BETA software package (version 1.0.7).For RNA-seq The human reference genome (hg19) was used to to align transcriptome-sequencing reads using STAR (version 2.7.1a). featureCounts (version 2.0.1) from GRCh37 Ensembl reference was used for counting.R package Edger (3.36.0) was then employed to to process all gene counts and evaluate the differential expression using the Benjamini-Hochberg false discovery rate (FDR)-adjusted P-value.The expression values were normalized by by centering and scaling across samples and displayed using the ComplexHeatmap (version 2.10.0)R package.Gene Set Enrichment Analysis (GSEA) was performed using Software GSEA (version 4.2.2) and R package fgsea (version 1.20.0).

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All the high-throughput sequencing data have been deposited in GEO under the accession number GSE232555 Patients with prostate cancer are of male sex, so no patients of female sex were included.
N/A race, ethnicity and socially relevant groups of the patients who donated tissue were not collected for this study.
N/A as this study used patient-derived xenografts (PDXs) from patient specimens that were obtained with informed consent All human tissues were obtained with informed, written consent by an independent clinical coordinator The studies were conducted under Human Research Ethics Committee (Institutional Review Board) approvals at Monash University (7996, 12287) and the Peter MacCallum Cancer Centre (15/98, 97_27).
Sample size was determined according to experimental design.No sample size calculation was necessary or performed.All biologic specimens available were used and included in the analysis No data were excluded.
Experiments were generally conducted with at lease three independent replicates, and these replicating experiments consistently yielded similar results.For ChIP-seq analyses in cell lines, two to three technical duplicates were performed and then merged for analysis.For ChIPseq analyses in PDX samples, a minimum of two biological replicates were performed.

Samples were randomly allocated
The experiments were performed blinded nature portfolio | reporting summary  ChIP-seq data were demonstrated to to be be of of high quality through various assessments.Fastqc was executed on on all samples to to confirm the presence of of good quality data.Additionally, the number of of peaks was considered, with a cutoff of of FDR <= <= 0.05.